After having major problems with getting q2map2 to run on 64bit linux I decided to get something working with Wine and a windows q3map2 binary as a temporary measure. In this package
is a folder containing the windows binaries, a map and a compile script. If you want to try it make sure you have wine installed. Edit the settings in the compile script to point at your own folders and binaries. Then navigate into the folder with linux console and type...
The compile script should then compile the bsp, make a pk3, put it in the correct folder and run the map in the game. If this works for you then you can put your own maps in the folder and start compiling them too.